Dear Dr Anders,

Based on my readings I am willing to use DESeq to analyze my RNA-seq data. I found it very easy to follow your instructions written on the package vignette, and to work with it for one factor comparison. However, I am not sure if I am using it correctly to account for a second factor in the model. So, here are my two questions:

How do I compare two groups, accounting for a second factor in the model?  (it is not a factorial model that I am looking for)

Can I simply write:
The condition  names as
"Ax", "Ax", "Ax", "Ax", "Ay", "Ay", "Ay", "Bx", "Bx", "Bx", "By", "By", "By"

nbinomTest ( cds, “A”, “B”)

being A/B may main factor and x/y my secondary factor?

That is what I understood from the page 3 of the vignette

“> conds <- c( "T", "T", "T", "Tb", "N", "N" )
where \T" stands for a sample derived from a certain tumour type and \N" for a sample derived
from non-pathological tissue. The
rst three samples had a very similar histopathological phe-
notype, while the fourth sample was atypical, and hence, we assign it another condition (\Tb").
”

Can I test for interaction effect between two factors?

Thanks so much,
Fernando

Research Associate - PhD
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